Archive folder removal
Under IMAP, Archive is a special folder that cannot be removed in the Thunderbird GUI. It may be removed by stopping Thunderbird, and removing the /home/user/.thunderbird/profile/ImapMail/server/Archives.sbd folder and Archives.msf file. TODO: clarify when this works; it did not on Charles' personal PolarisMail account.
Thunderbird will rebuild .MSF files as needed if they are missing so no need to back them up.
If backups are incremental, big folders (documented below) can result in huge backup data volumes.
Thunderbird uses a single file for some folders: Drafts, Inbox, Sent and Trash. When they grow large, say > 250 MB, it is prudent to reduce their size:
From kb.mozillazine (http://kb.mozillazine.org/Compacting_folders): If the folder is severely corrupted, deleting the .msf file won't help much, and compacting the folder may just make things worse because Thunderbird can't reliably figure out where a message ends anymore. You'll typically run into this only with the Inbox folder. It's much more vulnerable to corruption because it frequently has both lots of messages and a high percentage of deleted (but not visible) messages. That's why it's recommended that you move messages you want to keep to other folders/child folders rather than keep storing them in the Inbox."